tbuckley/cabot-search huggingface dataset:
Abstract 642: CSF-1R+ macrophages control the gut microbiome-enhanced liver NKT function through IL-18
Authors: Chi Ma, Justin McCallen, John C. McVey, Qianfei Zhang, Benjamin Ruf, Kylynda Bauer, Sophie Wang, Chunwei Walter Lai, Giorgio Trinchieri, Jay A. Berzofsky, Firouzeh Korangy, Tim F. Greten
Journal: Cancer Research (2023)

Abstract The gut microbiome is an important modulator of the host immune system. Here, we found that altering the gut microbiome by oral vancomycin increases liver NKT cell function. Enhanced NKT cytokine production and activation marker expression were observed in vancomycin-treated mice following both antigen-specific and antigen-independent in vivo NKT stimulations, with a more prominent effect in liver as compared to the spleen. Fecal transplantation studies demonstrated that the NKT functional regulation is mediated by altering the gut microbiome but uncoupled from the modulation of NKT cell population size. Interestingly, when stimulated in vitro, NKT cells from vancomycin-treated mice did not show increased activation, suggesting an indirect regulation. NKT cells expressed high levels of IL-18 receptor, and vancomycin increased the expression of IL-18 in the liver. Blocking IL-18 by neutralizing antibody or using genetically deficient mice attenuated the enhanced NKT activation. Liver macrophages were identified as a major source of IL-18. General macrophage depletion by clodronate abolished this NKT activation. Using anti-CSF-1R depletion or LyzCrexCSF-1RLsL-DTRmice identified CSF-1R+ macrophages as a critical modulator of NKT function. Together, our results demonstrate that the gut microbiome controls liver NKT function via regulating CSF-1R+ macrophages to produce IL-18. Citation Format: Chi Ma, Justin McCallen, John C. McVey, Qianfei Zhang, Benjamin Ruf, Kylynda Bauer, Sophie Wang, Chunwei Walter Lai, Giorgio Trinchieri, Jay A. Berzofsky, Firouzeh Korangy, Tim F. Greten. CSF-1R+ macrophages control the gut microbiome-enhanced liver NKT function through IL-18 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 642.
Abstract 5843: miR-224 activates cancer-associated fibroblasts to promote cancer cell invasion in lung tumor microenvironment
Authors: Seonyeong Oh, Inyoung Cheon, Young-Ho Ahn
Journal: Cancer Research (2023)

Abstract Cancer-associated fibroblasts (CAFs) promote EMT (epithelial-mesenchymal transition), invasion, and metastasis of cancer cells in the tumor microenvironment. To identify microRNAs (miRNAs) associated with the reprogramming of normal lung fibroblasts (LFs) into CAFs, global miRNA expression was profiled in LFs and CAFs through Nanostring nCounter. miR-224 was one of the increased miRNAs in CAFs, and its expression was higher in tumors than in normal tissues in dbDEMC and TCGA_lung adenocarcinoma data. miR-224 levels were then checked by qRT-PCR in paraffine-embedded tumor samples from patients with lung adenocarcinoma. Kaplan-Meier survival analysis showed that high miR-224 expression was related to poor survival. These data show that lung cancer progression is promoted by miR-224. To discover the roles of increased miR-224 in CAFs, miR-224 was overexpressed by lentiviral infection in LFs. LF_miR-224 overexpression enhanced the expression of CAF activation markers including Fap, S100a4, and Vim. In spheroid invasion assay using co-culture of LFs and cancer cells, as an experimental model of the tumor microenvironment, LF_miR-224 promoted invasion of lung cancer cells compared with control LFs. In transwell migration assay, LF_miR-224 stimulated migration of lung cancer cells more than control LFs. Collectively, these results indicate that CAFs reprogrammed by miR-224 promote the migration and invasion of lung cancer cells. Citation Format: Seonyeong Oh, Inyoung Cheon, Young-Ho Ahn. miR-224 activates cancer-associated fibroblasts to promote cancer cell invasion in lung tumor microenvironment. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5843.
Abstract 4778: Novel bioluminescence approaches for measuring fatty acid β-oxidation and production of reactive oxygen and nitrogen species
Authors: Kim Haupt, Matt Larsen, Hui Wang, Natasha Karassina, Mike Valley, Wenhui Zhou, Jolanta Vidugiriene
Journal: Cancer Research (2023)

Abstract Energy uptake and utilization in eukaryotic cells is a dynamic process regulated by a series of interacting metabolic networks. Interrogation of this complex network relies on rapid, sensitive approaches that do not require extensive sample handling and are easily adaptable to 96- and 384-well plates. Previously, using the Ultra-Glo luciferase reaction we developed a panel of bioluminescent assays that can be used to monitor numerous aspects of cellular metabolism and mitochondrial function including ATP production, glucose and amino acid metabolism, and the TCA cycle. Here, we extend the use of the luciferase reaction and report on the development of novel bioluminescence probes for studying two important metabolic cellular responses: fatty acid β-oxidation (FAO) and production of reactive oxygen and nitrogen species. For studying FAO, we developed a cell permeable probe with caged-luciferin attached to a fatty acid chain. The probe enters the cells and following FAO cycling, free luciferin is released and detected using Luciferin Detection Reagent. We validated the approach using known FAO activators and inhibitors and used it to monitor the changes in FAO during T-cell activation. For measuring reactive oxygen and nitrogen species, highly selective bioluminescence probes were developed. Upon reaction of the probes with their corresponding ROS target, they form the stable D-luciferin reporter molecule, causing luciferin to accumulate. Upon treatment with luciferase in the detection step, the generated light allows for quantification of the superoxide or nitric oxide formed. Both probes are suitable for in vitro and cell-based detection of ROS in an “add and read” format, providing for a simple workflow amenable to high throughput experimentation. Citation Format: Kim Haupt, Matt Larsen, Hui Wang, Natasha Karassina, Mike Valley, Wenhui Zhou, Jolanta Vidugiriene. Novel bioluminescence approaches for measuring fatty acid β-oxidation and production of reactive oxygen and nitrogen species. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4778.
Abstract 2606: Requirement of MDM2 E3 ligase activity for regulating p53 during normal development, cell cycle regulation and genome integrity
Authors: Meenalakshmi Chinnam, Rati Lama, Chao Xu, Xiaojing Zhang, Carlos Cedeno, Yanqing Wang, Aimee B. Stablewski, David W. Goodrich, Xinjiang Wang
Journal: Cancer Research (2023)

Abstract p53 tumor suppressor, the most mutated gene in human cancer, is negatively regulated by MDM2 and MDM4 proteins. Two distinct mechanisms of MDM2/MDM4 regulation of p53 include, one, suppression of p53 transactivation activity by direct interaction of MDM2/MDM4 with p53 protein, thus blocking its transactivation interface and two, targeting p53 to proteasomal degradation by MDM2 E3 ligase activity. However, the importance of these mechanisms in normal p53 regulation in vivo has remained controversial. To genetically separate these two mechanisms of p53 regulation we generated a novel Mdm2 mutant mouse (Mdm2L466A) that lacks E3 ligase activity but retains the ability of Mdm2 to heterodimerize with Mdm4 and inhibit p53 transactivation. Homozygous Mdm2L466A mice are embryonic lethal due to dysregulated p53 activity, thus demonstrating Mdm2 E3 ligase mediated regulation of p53 is essential during embryonic development. Additionally, we uncovered novel p53-independent functions of MDM2 E3 ligase in cell cycle regulation and genome integrity in cells. Cells lacking MDM2 E3 ligase activity have defective G2-M transition during cell cycle and developed elevated levels of aneuploidy regardless of p53 status. This study unequivocally demonstrates the requirement of Mdm2 E3 ligase activity for normal regulation of p53 and uncovers previously unknown p53-independent role of Mdm2 in cell cycle regulation and maintaining genome integrity. A current therapeutic approach involves blocking MDM2-p53 interaction to promote p53 tumor suppression function in cancer cells. Our findings suggest that this approach alone is insufficient because MDM2 has other potential oncogenic mechanisms independent of its role as negative regulator of p53. Hence, targeting MDM2 E3 ligase activity is likely to be more effective cancer therapy as it addresses both p53-dependent and p53-independent oncogenic mechanisms of MDM2. Citation Format: Meenalakshmi Chinnam, Rati Lama, Chao Xu, Xiaojing Zhang, Carlos Cedeno, Yanqing Wang, Aimee B. Stablewski, David W. Goodrich, Xinjiang Wang. Requirement of MDM2 E3 ligase activity for regulating p53 during normal development, cell cycle regulation and genome integrity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2606.
Abstract 3600: MET-mediated STING activation regulates EMT and NF-ΚB pathway in non-small cell lung cancer
Authors: Seungchan Mun, Bogyeong Han, HyunKyung Ahn, Jaemoon Koh, Sehui Kim, DooHyun Chung, YoonKyung Jeon
Journal: Cancer Research (2023)

Abstract The cyclic GAMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway is known to have anti-tumor activity by activating the innate immune response against cytosolic double-stranded DNA (dsDNA). The regulating mechanism of STING remains unclear, and a pro-tumorigenic effect of STING pathway was recently reported. In this study, we investigated the expression of STING by MET and a novel role of the STING pathway in non-small cell lung cancer (NSCLC). The Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE) analysis showed that cGAS/STING pathway is enriched and STING expression is higher in MET-overexpressing tumors. Western blot for NSCLC cells and immunohistochemistry for NSCLC tumor tissues showed positive correlation between MET and STING expression in NSCLC cells. MET-overexpression and a MET agonist (HGF) treatment increased STING expression and CXCL10 and IFNβ expression and secretion, whereas MET-knockdown and a MET inhibitor (capmatinib) treatment decreased STING expression in NSCLC cells. In MET-positive and STING-positive cells, a STING agonist (poly-dAdT and diABZI) treatment led to increased activation of STING signaling pathway. In EBC-1 cells, MET knockdown decreased STING expression and STING-agonist-induced STING-pathway activation and cytokine production. To further investigate the role STING in NSCLC, EBC-1 cells were transfected with STING siRNA and submitted to RNS-seq. Gene set enrichment analysis revealed that several pathways were affected by STING expression. Epithelial-mesenchymal transition (EMT) and TNFα-signaling via NF-κB signaling were significantly downregulated in STING-knockdowned cells. In vitro experiments using EBC-1 cells, STING overexpression increased SLUG and TWIST1 expression and migration of cells, whereas STING knockdown decreased SLUG and TWIST1 expression and migration of cells. In summary, this study demonstrated that MET and STING expression were positively correlated with each other in NSCLC and MET overexpression increased STING expression and subsequent activation upon STING agonist stimulation. In addition, STING contributed to EMT in NSCLC. Citation Format: Seungchan Mun, Bogyeong Han, HyunKyung Ahn, Jaemoon Koh, Sehui Kim, DooHyun Chung, YoonKyung Jeon. MET-mediated STING activation regulates EMT and NF-ΚB pathway in non-small cell lung cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3600.
Abstract 5328: Novel KRAS-specific in-well lysis ELISA for high throughput screening
Authors: Hyun Min Park, Jason Poole, Mary Anne Jelinek
Journal: Cancer Research (2023)

Abstract RAS is one of the most frequently mutated genes in cancer. Gain–of–function missense mutations promoting oncogenesis cluster at codons 12, 13, and 61 of KRAS, NRAS and HRAS. These result in enhanced GTP binding due to fast exchange of nucleotide and/or impairment of GAP (GTPase Activating Protein) binding. Although these mutants are all activating, they are not equal in their oncogenic potential and differences in patient survival are associated with different RAS mutants and which RAS allele is affected, with KRAS being the most prevalent. Current RAS therapeutic approaches have migrated to be isoform specific. With this in mind, we have developed an activation state specific high throughput screening compatible (HTS) assay that is specific for KRAS. A novel rabbit anti–KRAS recombinant antibody was isolated via cloning of immunoglobulin variable regions from antigen positive B cells isolated from rabbits immunized with a peptide immunogen targeting a region of low homology between the RAS isoforms. Antibody specificity was validated with recombinant HRAS, KRAS and NRAS proteins over a wide concentration range by both immunoblotting and by a bead–based multiplex ELISA where all three RAS isoforms were present. The new assay allows for direct in–well lysis of cells cultured in 96–well plate format, either directly in media or following a PBS wash step. Activated KRAS in the lysate is captured on the assay plate and detected via chemiluminescence using the KRAS specific antibody. Preliminary assay validation has included EGF treatment of HeLa cells to show activation in cells expressing wildtype KRAS and inhibition with the selective non–covalent KRASG12D inhibitor MRTX1133 in Aspc1 cells known to express KRASG12D over a wide range of cell seeding densities. We anticipate that this assay will further the discovery of novel KRAS specific therapeutics. Citation Format: Hyun Min Park, Jason Poole, Mary Anne Jelinek. Novel KRAS-specific in-well lysis ELISA for high throughput screening. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5328.
Abstract 6693: Stability of urinary cell-free DNA and detection of T790M variant
Authors: Carolin Münch, Saikal Shamkeeva, Mitja Heinemann, Berend Isermann, Sabine Kasimir-Bauer, Bahriye Aktas, Ivonne Nel
Journal: Cancer Research (2023)

Abstract Background: The so-called “liquid biopsy” has become a powerful tool for cancer research in the recent years, with circulating cell-free DNA (cfDNA) that originates from tumors as one of the most promising analytes. In contrast to plasma derived cfDNA, only a few studies were performed investigating urinary cfDNA. One reason might be quick degradation and hence relatively low concentrations of urinary cfDNA. This study focused on examining the stability of cfDNA in urine using different ways of preservation under various storage conditions. Methodology: To mimic patient samples, a pool of healthy male and female urine donors was spiked with a synthetic cfDNA reference standard (fragment size 170 bp) containing the T790M mutation in the EGFR gene and preserved with three different buffers and no buffer over four different storage periods (0; 4; 12; 24 h) at room temperature vs. fridge. Preservatives used were the Urinary Analyte Stabilizer (UAS, Novosanis), the Urine Conditioning Buffer (UCB, Zymo) and a self-prepared buffer called “AlloU”. The cfDNA was extracted with the QIAamp MinElute ccfDNA Mini Kit (Qiagen) and the concentration measured with the Qubit™ 4 fluorometer (Thermo Fisher Scientific). Droplet digital PCR (ddPCR) was used for detection and quantification of the T790M mutation (Bio-Rad) Results: From the model samples with no preservation buffer, almost no spiked cfDNA could be recovered and the T790M variant could not be detected using ddPCR, indicating that without preservation cfDNA was degraded below the detection limit by the nucleases present in urine. The most effective stabilizing buffer over all storage periods and at room as well as fridge temperature was the UAS, resulting in accurate detection of the T790M variant using ddPCR. Conclusion: From a technical point of view, urinary cfDNA might be useful for non-invasive disease monitoring when the samples are stabilized and stored adequately during clinical routine. Citation Format: Carolin Münch, Saikal Shamkeeva, Mitja Heinemann, Berend Isermann, Sabine Kasimir-Bauer, Bahriye Aktas, Ivonne Nel. Stability of urinary cell-free DNA and detection of T790M variant. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6693.
Abstract 5869: The concordant disruption of B7/CD28 immune regulators predicts the prognosis of oral carcinoma
Authors: Sih-Rou Chang
Journal: Cancer Research (2023)

Abstract Immune-escape is a critical factor determining the survival of malignancies including oral squamous cell carcinoma (OSCC). The immune escape of cancer cells may be driven by B7/CD28 family members and others on the tumor cells that form ligand-inhibitory receptor complexes with immune cells. Since the family members of B7/CD28 can functionally compensate, the concomitant disruption of multiple B7/CD28 family members in OSCC pathogenesis remains elusive. RNAseq performed on OSCC and paired oral mucosa retrieved the transcriptome of OSCC, and algorithms signified the general alterations of T cell population and the increase of macrophage population in tumors relative to controls. Upregulation of CD80, CD86, PD-L1, PD-L2, CD276 and CTLA4, and downregulation of L-ICOS in OSCC relative to normal mucosa was noted. In addition, there was a high concordance in the expression profile across the dysregulated regulators. The co-upregulation of CD276 and CTLA4 was associated with the decrease of T helper and NK cell population, and the increase of Treg and myeloid dendritic cell population. Interestingly, tumors harboring higher PD-L1 and/or PD-L2 expression accompany with lower ICOS or PD1 expression exhibited worse prognosis. In combination with these immunity features in primary tumors, the survival of patients with lymph node metastasis was further worsened. In the isografic models of murine OSCC cell lines, the decrease of CD4+T population in the lymph node and increase of myeloid dendritic cell population in the spleen were induced in the host mice. Many miRNAs are involved in the modulation of immune escape for malignancies. With the treatment of inhibitors against oncogenic miRNAs which enabled the OSCC suppression, the inhibitors of miR-146a and miR-211 also resulted in the down-regulation in the protein expression of multiple B7/CD28 members. This study concludes the eminent co-disruption of B7/CD28 members in OSCC tumors, which would confound the patient survival. The efficacy of miRNA inhibitors in abrogating oncogenicity and B7/CD28 members could be a therapeutic strategy. Citation Format: Sih-Rou Chang. The concordant disruption of B7/CD28 immune regulators predicts the prognosis of oral carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5869.
Abstract 216: Profiling single cell and spatial transcriptomes in FFPE archived tissues
Authors: Jasmine Ying-Jiun Chen, Quynh Le, Chris Kang, Roy Tam, Brian Tai, Kelly Lo, Nasim Rahmatpour, Perry Wasdin
Journal: Cancer Research (2023)

Abstract Single cell and single nuclei RNA sequencing (scRNA-seq and snRNA-seq) have helped to identify cell type and subtypes that are present in complex tissues in both healthy samples and disease states. So far, scRNA-seq and snRNA-seq can only be performed in fresh tissues, or fresh frozen tissues. Most archived tissues are formalin-fixed, and paraffin-embedded (FFPE), making them inaccessible to the modern technology for characterization. Recently, 10x Genomics release a new reagent enabling single-cell fixed RNA characterization from fixed samples. The initial release is for fresh samples being fixed and then profiled later. However, FFPE archived tissues are not supported yet. We showed here two protocols to dissociate single cells and single nuclei from a 10-year-old FFPE human gastric tumor. We then profile them with 10x Genomics’ fixed RNA profiling kit. We further compare the data with the 10x Genomics’ Visium data obtained from the same tissues to understand the performance of these two protocols. In summary, we show that such technology will help to further characterize archived tissues that already have pathology annotation as well as clinical data and help biomarkers identification. Citation Format: Jasmine Ying-Jiun Chen, Quynh Le, Chris Kang, Roy Tam, Brian Tai, Kelly Lo, Nasim Rahmatpour, Perry Wasdin. Profiling single cell and spatial transcriptomes in FFPE archived tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 216.
Abstract 4381: Predictive risk factors for cancer thrombosis in gastric cancer patients
Authors: Song Ee Park, Moon Ki Jung, In Gyu Hwang
Journal: Cancer Research (2023)

Abstract Background Gastric cancer is strongly associated cancer thromboembolism. We aimed to identify the Khorana risk score (KRS) and other risk factors for cancer thromboembolism in patients with gastric cancer after gastrectomy. Methods We reviewed 610 gastric patients, who had undergone D2 radical gastrectomy between January 2005 and December 2017. Kaplan-Meier survival analysis and Cox regression models were used to evaluate for independent predictor of cumulative incidence of cancer thromboembolism and survival. Results The median follow up was 67.0 months. There were 35 (5.7%) caner thromboembolism. The cumulative incidences of thromboembolism were 6.1%, 3.1%, 3.3%, and 20.7% in stages I, II, III, IV. 181 (29.7%) patients were relapsed cancer and 159 (26.1%) patients were died. A high KRS (cumulative incidence 5.8%) was not associated with cancer thromboembolism compared to an intermediate KRS (cumulative 5.7%) (HR=1.005, 95% CI = 0.540-2.061, P= 0.876). After gastrectomy, recurrent cancer (cumulative incidence 9.9%) was associated with cancer thromboembolism compared to no recurrence (cumulative incidence 4.0%) (HR 3.713, 95% CI 1.879-7.335, P &amp;lt; 0.001). Conclusions Recurrent gastric cancer patients after gastrectomy were significantly increased cancer thromboembolism risk compared to no recurrent cancer patients. Among patients with gastric cancer after gastrectomy, KRS did not stratify the patients at high risk of cancer thromboembolism. Citation Format: Song Ee Park, Moon Ki Jung, In Gyu Hwang. Predictive risk factors for cancer thrombosis in gastric cancer patients. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4381.